Knowing the Difference
by 4JACE
Summary: Power struggles. Spoilers for 2x08 Conversion. JE.
1. Chapter 1

**Content Warning** - This first part has a bad word in it.

She went to her room a half-hour before they were due to return. Over the past months it had developed into an unplanned ritual, a superstitious act of faith that provided her with a few minutes away from the eyes of those who looked to her for guidance. It was her sanctuary: a few brief, precious moments of privacy for bargaining with God. In those moments she waited, she prayed, she pictured their faces in her mind...and she tried not to think about what she would do if they didn't come home. She supposed she should feel guilty for taking this time, for putting these ones above the others in her heart. She did not. This was _her _time; these were _her _people in a way that even the others were not. These moments, this heartache came from the intimacy of her soul, and she would not apologize for being human.

Her staff never disturbed her during these sessions. She hadn't needed to ask; they had understood and had taken it upon themselves to give her this time alone. They didn't even contact her as the scheduled activation drew near; she knew to the second when it would be and always returned to the command center with five minutes to spare. She was blissfully, gratefully alone for twenty-five minutes...to hope, to plead, to anticipate. This time was sacred. At least, it had been until now.

She stared angrily at the note that she had found slipped under her door. The letters were uneven, the message crude: _Go home, Bitch_. The shock of it stole her breath; she could feel her ribs pressing painfully beneath her skin. It wasn't the first hateful comment she had received, and it wouldn't be the last. As leader of Atlantis she couldn't please everyone all the time. She had made enemies, some of whom weren't the slightest bit hesitant in giving Fury a voice. She had ignored the others, as she should do with this one. For some reason it was harder this time. She wondered if it might be because the note had intruded on her solitude, on a time that was supposed to be hers alone. She thought to herself that it wasn't just that. There was something malevolent about this message, something truly unsettling. Maybe it was the handwriting, the way the large scrawl of red ink slasked across the page. Maybe it was the undiluted hatred of the tone. There was just something so _wrong_ about it...

She shook her head briefly and dropped the note on her desk. She was making too much of this, letting her private fears affect her judgment. She could use the city's systems to solve this mystery, of course. It would be easy enough to pull up the record of who had been outside her door this morning, who had stopped for a moment to deliver an angry missive to its intended target. Atlantis saw everyone and everything. Elizabeth wasn't sure she wanted to do that; she'd never done it that way before. It was her belief that a little rebellion was good for the soul...and good for the city. People had to be allowed to express their frustrations without fear of repercussion. Granted, she preferred civilized discussions in her office to anonymous hate mail in her private quarters, but she wouldn't be choosy. Besides, if she responded to this with any show of strength, wouldn't she be validating it by default? There was also Caldwell to consider; she couldn't afford to give the impression that she was weak, easily frightened...unfit for command.

The thought of command reminded her; with a glance at the clock, she realized that it was time to return to her duties. Leaving the note on her desk, she tucked the matter away in a compartment of her mind. The problem and its solution, if any, would just have to wait. She had something infinitely more important to do.

SGA--SGA--SGA

As she stood in the command center, able to breathe deeply for the first time since they left four days ago, she acknowledged that the group that had just walked through the Stargate was special to her. Teyla: beautiful, strong, and intelligent. Elizabeth respected and admired her; they were friends, even if certain factors in their relationship prevented them from being closer. Elizabeth admitted to herself that there was uncertainty involved, as well as a good dose of envy that she had absolutely no business feeling.

She turned from that thought before it could fully form and studied the other members of the group. Ronon: strong warrior and unpredictable element. Of the four, he was the one she knew least. She accepted that he was a valuable asset to the team and to Atlantis, but she wasn't naïve enough to think that he played by the same rulebook as everyone else. Due to loyalty, he could be trusted. For now.

Rodney was being his usual, slightly annoying self. He had been talking when he walked out of the gate, and he continued to do so. She listened with amusement, wondering how anyone could string that many multi-syllabic words together that quickly without choking. He was absolutely brilliant in his field (and better than 99.9 percent of the population at just about anything, he would claim). More importantly he was a good man with a kinder heart than most people realized, and he was more courageous that he believed himself to be.

While she had made peace with her feelings for this team, she was still uncomfortable admitting, even to herself, that the fourth person was more important to her than the others, more important than anyone she had ever known. She'd given up trying to deny it a few months ago, but that didn't mean she had to like it or act upon it. John Sheppard appeared to be listening with full attention to Rodney's chatter, but his eyes had been searching the command center from the moment he stepped through the gate. His gaze locked with hers and he nodded, so slightly that Elizabeth was sure nobody else even noticed. It was a private communication, meant only for her to understand: _I'm here, and you're where you ought to be, and we're both safe and whole_.

It was in response to that unspoken thought that she smiled and said warmly, "Welcome home."

He grinned up at her and replied, "It's good to be back. You're going to just _love _what we found on our trip." His eyes were bright, and the message they conveyed now was _Do I have the coolest job in the universe, or what?_

They had found something important. She could see it on all of their faces, and the enthusiasm was contagious. She answered with as much cool professionalism as she could muster because she knew he got a kick out of it. "I'm sure it will be very interesting. We'll meet in the conference room after you check in with Dr. Beckett."

He made an appropriately sarcastic remark about doctors and moms before leading his team away. She stepped into her office to hide a smile and devoted herself to paperwork for the next hour.


	2. Chapter 2

"ZPMs," John announced triumphantly. "A lead on at least three, possibly more."

"You're sure the information is valid?" Elizabeth asked skeptically.

"As sure as we can be," Rodney replied. "The Brenye are technologically advanced but have always chosen to live simply, using nature to supply their needs. Why anyone would choose to live that way escapes me, when the advent of technology--"

"Rodney," Elizabeth said firmly.

He nodded. "Right. Anyway, about fifty years ago a research expedition on the far side of the planet discovered some items that look like ZPMs from the schematics I was shown. Their scientists theorized that they could be used as an energy source, but the conservatives in the group wanted to continue using the natural methods...water, wind, Mother Planet, Father Sky...that had been practiced for as long as anyone could remember. Eventually the colony divided; the forward-thinkers took the ZPMs and gated to another planet while the traditionalists remained on the home world and played 'Look! I'm an ostrich!' " Seeing their confusion, a pained expression flitted across his face as he sighed and tried to explain. "You know: bury our collective heads in the sand, pretend not to notice as technology passes us by..."

_"In any case,"_ John interrupted as he cast a quelling glance at the scientist, "the Brenye who have remained on the planet have recently begun contacting other races and would like to meet with us. We might have some medical supplies they would be interested in, but I think what they want most of all is the chance to talk to our people."

"And in exchange they'll give us the gate address the other Brenye used when they left?" It sounded almost too easy, but years of diplomatic service had taught her that treasure truly did lie in the eye of the beholder.

Rodney nodded eagerly. "Their records mention at least three ZPMs that were taken during the disagreement, but some of the documents are missing. It's conceivable that there might have been more."

Teyla's eyes were cautious. "There is one aspect to the arrangement that might not be to your liking, Dr. Weir."

Elizabeth lifted an eyebrow and looked to John for an explanation. His face serious now, he said, "The Brenye want to meet you personally. Leadership is very important to them, and they want to honor you during a visit to their colony."

Caldwell immediately objected. "It's too risky. As leader of Atlantis, you should remain in the city where you can be protected."

"I agree," John said with exaggerated patience. Elizabeth listened with amusement. That tone, she was sure, was part of the reason John had struggled as much as he had in the Air Force. He continued, and she found that she didn't like what she heard. "I think we should try to convince the Brenye to meet here first. We can always visit the colony later if we decide it's safe."

Elizabeth narrowed her eyes. "So we're denying one of their requests before negotiations have even begun?" She looked across the room at Teyla. "You knew of the Brenye; that was the reason we decided to visit the planet. Can they be trusted?"

"The tales I was told as a child were of events long past and did not have much detail. I believe the division between the two groups was handled in a peaceful manner." Teyla tilted her head to one side, a thoughtful look on her face. "I sensed no deception during our visit."

"If you decide to go, a group can travel ahead to set up security," Ronon said. It was clear that he intended to be among that group.

Elizabeth looked at John. "Can you give me any concrete reason why you think it wouldn't be safe to go?" All of the sudden she had discovered that it mattered very much that the initial meeting take place at the Brenye colony. She wanted to go; she hadn't been away from Atlantis in a long time. Her eyes sparkled with longing, and she knew John noticed. She knew what he would say before he began to speak."

"No. I think it's safe enough, and we can detail security teams to protect you." His eyes met hers with their shared enthusiasm.

Caldwell protested, "I still think--"

"It's decided," Elizabeth said firmly. "Colonel Sheppard, make arrangements for the necessary security measures. We'll leave as soon as it's convenient for our hosts."

John nodded. "I'll send two teams ahead to arrange security. Ronon, Teyla, I want you to go with them."

"I'd like to attend the negotiations as well," Caldwell interjected. Before Elizabeth could respond, he added, "Unless you need me to command Atlantis while you're gone."

_Not in this or any other lifetime._ "Of course you're always welcome to travel with us when you're on Atlantis, Colonel," Elizabeth said with deceptive calm. "We'll leave as soon as the security team sends word that arrangements have been made." Caldwell wasn't a bad man, but he was ambitious. So was she...and she'd been here first.

SGA---SGA---SGA

She waited for him on the balcony near her room; this, too, had become a ritual for them over the past few months. At first they had met in private to discuss mission details that required discretion. Then he had begun to describe the worlds he had visited; she had listened with fascinated interest, sometimes with delight and other times in horror. On the terrible occasions when he had returned through the gate injured, she had sat by his bed in the infirmary and listened to his agonized whispers. Her poor bedside manner was an ongoing joke between them, but she had overcome her discomfort and sat with him anyway. When she had noticed how tired he was after each trip and how he tried to avoid contact with other people, she had arranged to have a meal waiting on the balcony so that he wouldn't have to face the crowd. The pleasure on his exhausted face had almost broken her heart, and she'd made the effort to have dinner for him ever since.

Tonight he was in a good mood, relaxed and pleased about the possible ZPM leads. She had only been waiting a short while when he stuck his head around the doorway and teased, "You just _had_ to bring Caldwell along to spoil the party, huh?"

She turned to face him, her brow raised. "You would have preferred for me to give him unsupervised control of Atlantis?"

He shuddered. "I'm freaking out just thinking about it."

Elizabeth flinched as the words reminded her of another time, a desperate time. _That freaks me out more than anything._ It had been a different John Sheppard who had said those words, a frightened mixture of perfected soul and fragile DNA who had looked at her with barely concealed panic in his eyes...

She realized that he was calling her name, concerned. "Are you okay?"

She swallowed hard but couldn't quite find her voice. "I'm fine," she murmured.

His eyes were too intent, too knowledgable. "You're sure?"

Carefully tucking away her emotions, she nodded. "Yes," she said, her voice stronger this time.

He didn't look convinced, but he took the hint. Giving her a final, searching look, he moved past her to take a plate and began selecting food from the tray she had brought. "Thanks for the meal, as always."

"You're welcome, as always." She studied his profile, doing her own inventory to make sure that he was unharmed. "How was your trip?"

"Good," he mumbled around a mouthful of food. He grabbed the beer she offered him (from a private stash that she kept solely for this purpose) and took a quick drink. "It's a long walk to the colony, though...almost ten miles. Be sure to wear comfortable shoes."

She smiled as she watched the sun go down over the horizon. "I guess I'll leave my heels at home this time."

His reply was so quiet that she almost didn't hear it. "Too bad."

She turned quickly, but he was eating from his plate as if nothing unusual had occurred. Taking a low breath, she said, "So...ten miles."

He nodded. "The colonists were loners for a long time, remember? No need to be near the stargate if you aren't planning to use it. It's a nice walk, though; you'll like it. There's a river...starts about five miles in, leads straight to town."

"Sounds pretty," she said, intrigued.

"It is. You picked a good time to get cabin fever." The twinkle in his eye told her that he knew exactly why she had been so adamant that she meet the Brenye on their own turf. She felt the corner of her mouth quirking in response before remembering that there was something she had wanted to ask him.

"Why did you agree to let me go?"

He looked at her speculatively. "Are you saying you would've listened if I had insisted that you stay here?"

"No," she said promptly, smiling, and then continued more seriously, "but you would normally would have fought harder. Why did you give in?" She knew that no matter how much she might want...need...to have some time off from Atlantis, he would never have agreed if it went against his better judgment.

He shrugged. "I really do think you'll be safe. These people...there's just something about them. I don't know how to explain it any better than that."

"Okay," she said easily, trusting him

"You'll like the town," he promised. "Lots of creativity, culture...that sort of thing. You should check out the artisan's market while you're there."

"I will, if we get any free time," she replied. He didn't tell her that she could set her own schedule; he knew as well as she did that leaders often face more limitations than the people they lead.

They talked for a long time, enjoying the quiet warmth of the night air. When she finally returned to her room she was startled to see the note lying on her desk; she'd forgotten all about her mysterious enemy. In the light of the day's discoveries and her pleasant evening with John, her fears about the note and its author seemed exaggerated. She crumpled the paper up and threw it away, determined not to give it another thought. She went through her evening routine and slipped into bed, excited about the upcoming trip. If she dreamt about walking by a river with her second in command, it was nobody's business but her own.

TBC

A/N: I don't know if I write the best "mission fic" in the world, so please bear with me. Also, if an idea has been used before or I make some huge technological mistake, please let me know. I'm doing as much research as I can to make sure that I don't slip up, but it always happens anyway. :)


	3. Chapter 3

Caldwell walked beside her for the entire trip to the Brenye colony. She might have tried to slip away if she hadn't noticed the relieved looks on the faces of her people. As long as he was talking to her, he wasn't bothering anyone else. Rodney would have gone out of his way to annoy the man, Ronon didn't trust him, Teyla barely tolerated him ever since he had made it clear that Sheppard's life was expendable, and John...well, ten miles of John Sheppard having to play nice with Steven Caldwell would have required more miracles than the Pegasus Galaxy had hungry Wraith. So Elizabeth stayed by his side, discussing events from both home and Earth.

Occasionally she looked around at the group, watching how they interacted with each other. They had been met at the gate by members of the security team, some of them from Atlantis and others from the Daedalus. The latter had been an offer by Caldwell, another subtle maneuver that she couldn't refuse without creating more trouble than she needed. John's eyes were everywhere: studying the perimeter, ensuring that the people under his command were doing their jobs. He was subtle about it, with a lightness of tone that kept people at ease, but he was also dead serious. He moved around a lot, checking in with various members of the expedition. He served as referee for one of Rodney and Zelenka's inevitable arguments before moving away to walk with Carson for awhile. When the group broke for lunch she watched him settle beside Teyla; whatever he said to her made her smile. Elizabeth cast a concealed glance at the albatross who was sitting beside her, obliviously eating an MRE, and sighed. Sometimes being the leader sucked.

Even as she thought it, she shook her head. It was just part of the job, a job that she loved dearly. She knew Caldwell struggled with the same feeling of isolation; it was one of the reasons that he sought her out for conversation. A little voice in her mind whispered that it wasn't the only reason, but she firmly squashed it. If she could keep her people happy by dealing with Caldwell, then she'd talk until she was blue in the face. He wasn't exactly bad company, anyway. He was intelligent and dedicated. If she could ignore the queasy feeling of spending several hours in the company of someone she couldn't trust, then she actually had a decent time. When they reached the river John had talked about she let the water calm her, the gentle sound reminding her of Atlantis. She was glad when they reached the colony. It was late when they arrived; she participated in the necessary introductions and retired to her room as soon as possible to prepare for the next day.

The initial meeting went well. The Brenye were a quiet group of people who exuded peace. They tended towards a slender build laced with wiry strength that could only come from having lived off the land for many years, and they had the most beautiful eyes she had ever seen. The prevailing color seemed to be light green, with the occasional blue or pale grey added to the mix. What made their eyes so delightful wasn't the color, however, it was the contentedness that shone from within them. The Brenye were at peace with themselves, and it was unbelievably calming.

The meeting room they were led to was a reflection of its creators: simple, functional, and incredibly beautiful. There was an elegance about the entire place, a feeling of having lived a certain way for a very long time and having become very good at it. Elizabeth slipped into her chair with a feeling of homecoming; this was the part of her job that she loved the most. She was prepared to reach out a hand of friendship to these people, to learn some of their secrets and share the best parts of her world with them. This was her highest purpose, and she never, ever got tired of it.

It was interesting to watch the reactions of her people as the day progressed. It wasn't as obvious with Teyla or Carson because they ware always gentle spirits, but the others were decidedly better behaved than usual. The peaceful atmosphere seemed to have rubbed off on them. Rodney wasn't talking a mile a minute, didn't challenge Zelenka with every other breath, and had even stopped to listen politely when the Brenye scientists spoke. There appeared to be no trace of the sarcastic arrogance from a few days earlier in Atlantis. Elizabeth knew that John had to be bored half to death with the negotiations because the Brenye needed nothing in the way of military training or weaponry, but he didn't show it at all. There were no fidgity hand movements, no wisecracks...just exemplary manners and an apparently limitless supply of patience. Caldwell had miraculously stayed quiet and supportive throughout all of the discussions, and even Ronon seemed softer around the edges. Elizabeth wondered if she could arrange to take some of this peaceful spirit home with them as part of the trade agreement. Would they need to take an actual Brenye, or could Beckett come up with some way to capture the essence in a bottle? Maybe he could even synthesize it...

With a start, Elizabeth realized that the Brenye leader, Arin, was apparently awaiting her response to something. Before she had time to panic, John came to her rescue. "We would be honored to have dinner with you this evening," he said smoothly even as he shot her a questioning glance. It was that wide-eyed look of his, and she could almost _hear_ his voice in her head: _It's not nice to daydream during the Very Important Meeting, Doctor._

She added her agreement to the dinner arrangements, steadfastly refusing to look at John again. They stood, pleased with the results of the day's work and looking forward to what would undoubtably be an excellent meal, if the lunch they had been served was any indication. It was as they were walking to the dining area that it happened: there was an outburst of angry voices at the other end of the hall and Elizabeth noticed that several people were having to be restrained. "Arin?" she asked quietly as John tensed by her side.

The Brenye leader was watching the events unfolding at the other end of the room. "I apologize, Elizabeth. There are those among us who questioned the wisdom of interacting with other beings. I thought we had addressed their fears--"

"Apparently you thought wrong." John's voice was dead even, a sure sign that he was about to get seriously pissed off. Elizabeth shot him a glance, warning him to tread carefully.

Arin sighed. "Apparently we did."

"Why didn't you mention this before?" John pressed, relentless.

The other man turned to meet John's angry glare. "I didn't realize there was a problem when you were here before. I knew that a few people had voiced opposition to your visit, but I thought it could be dealt with peacefully. You are the first outsiders we have had significant interaction with; I had no idea that the response of a few...a very few...colonists would be so volatile." For the first time all day, Elizabeth saw the peace in the man's eyes diminish; something inside her cried out at the loss. Before she could say anything, Arin responded to a gesture from someone across the hall. "I'm afraid I must ask you to excuse me for a moment. Please...stay. Enjoy your meal."

"Yeah right," John muttered under his breath as the other man walked away at a pace that was just short of a full-out run.

"John," Elizabeth said softly, not wanting to be overheard.

He turned to face her, his eyes dark and uncompromising. "He lied to me," he said, quietly furious.

"We don't know that," she countered.

His jaw clenched. "I trusted him. I brought our people here because of that trust; I brought _you_..." His voice had been increasing in volume as he spoke; now it died away as he looked at her, helpless.

She felt something warm take life in her heart. "And I'm here," she replied gently. "I'm here, and I'm safe. I'm _fine_. We'll finish the negotiations and return home, safe and sound."

He shook his head firmly. "We're returning home, alright. Right now."

"No, we're not," she countered.

"Elizabeth," he said warningly.

"No, John. We're here, and we'll finish the job we came to do. Besides," she continued, "what are we talking about, anyway? A few dissenters, a handful of people who don't like the current administration's policies? We have the same problem on Earth...and on Atlantis." For a moment she pictured a note with maliciously scrawled handwriting, but then she pushed the thought away. "If we allow, even encourage that freedom of speech from our own people, why should we expect any less from others?"

"We don't know that it's just speech," John argued.

"We don't know that it isn't," she fired back.

He studied her face, considering. Finally he sighed and ran a hand through his hair. "Do you think he's telling the truth?"

"It's hard to tell," she replied. "He seems to be sincere, but that's just appearances. Plus there's something about these people...something calming..."

He nodded. "You felt it too, then."

"Yes. The question is whether it's real or some kind of trick to soothe us into being careless." She sighed and shrugged her shoulders. "I just don't know. Diplomacy isn't an exact science."

He grinned, and she knew he was conceding the battle...for now. "No, it's not. However, dinner is about as exact a science as one could hope for. Feed John Sheppard...make him happy. Just be sure to avoid the Lygra grapes from Trielste because when he eats them he--um...you know what? Never mind."

Was he _blushing_? "You don't have to explain, Colonel Sheppard. I read the mission report, remember?" Yep, that was definitely a blush. Smirking, she walked past him and headed to the table. "Let's eat."


End file.
